One embodiment of the present invention provides a system that accommodates different clock frequencies in an EPON. The system receives a signal from the OLT at the ONU and derives an OLT clock. The system also maintains a local clock. The system further receives from the OLT an assignment for an upstream transmission window, during which the ONU can transmit an upstream data burst to the OLT based on the local clock. The system adjusts the number of bits of the data burst without affecting the payload data carried in the data burst, thereby allowing the data burst to fit properly within the upstream transmission window and compensating for frequency differences between the local clock and the OLT clock. The system transmits the data burst based on the local clock in the upstream transmission window.